A meteor shower bursts from the heavens, raining destruction on the unsuspecting citizens of Smallville, Kansas.

Clark meets Arthur "AC" Curry, a young man with extraordinary powers underwater. AC is in Smallville hoping to sabotage a Luthorcorp experiment that is threatening sea life. While in Smallville, AC forms an attraction to Lois.

Lana tells Clark that she is moving to the Metropolis University and she is accepted in the Tri Psi Sorority, a sisterhood with hot vampires led by Buffy Sanders, and Lana is transformed in a vampire. Meanwhile, the chief-editor of The Daily Planet, Pauline Kahn, denies an intern position to Chloe, but in the end she proposes Chloe to write a good story to prove that she might be part of the team of reporters. Meanwhile, Lex intimidates Professor Milton Fine, but in retribution he shows a dossier about the secret experiments that Luthorcorp is performing in the campus of the Kansas University. When Clark sees Lana at Chloe's room, he believes she is with a hangover; later, he goes with Lana to a Halloween costume party promoted by the Tri Psi. When Lana attacks Chloe, Clark discloses the truth about Buffy and her sisterhood of vampires and tries to find a means to save Lana and Chloe when she gets bitten by the evil vamp Lana.

While visiting Lana in Metropolis, Clark opens a package addressed to Lana apparently sent by Lex Luthor and is wounded and infected by a splinter of silver kryptonite. This unusual piece of kryptonite causes Clark to have paranoid delusions, and he sees Chloe, Jonathan, Martha, Lana and Lex plotting against him. He defends himself against his "enemies", jeopardizing the lives of his dearest friends and family. But eventually help comes from a most unlikely of source: Milton Fine.

While returning home with Lois, Martha is hit by a flash of light followed by a thunder and contracts a lethal Kryptonian disease. Clark fears that Jor-El thus makes him pay for his resuscitation and asks for help from Professor Milton Fine, who tells Clark that Jor-El was a dictator on Krypton, who destroyed their great leader General Zod and the planet but sent Clark to Earth to dominate the world; the death of Martha would only be prevented by destroying the Fortress of Solitude. Meanwhile, Lionel convinces Chloe to investigate who Milton Fine really is. When Lois, feeling offended because Lex called her a "muffin peddler", meets Chloe, the double visits LuthorCorp., where the truth is revealed: Professor Milton Fine is actually a Kryptonian artificial intelligence unit, created by Jor-El but re-programed and corrupted by the Kryptonian rebel General Zod, who was executed for treason, and had his spirit banished to the hell-dimension of the Phantom Zone. Fine, a Brain-Interactive-Construct (aka: Brainiac), is trying to trick Clark into releasing Zod's spirit from the Phantom Zone by destroying the Fortress of Solitude.

Simone, a gorgeous blonde, comes to Smallville hypnotizing Clark with a blue pendant ruining his relationship with Lana, as well as hypnotizing Martha and Lex.

Jonathan Kent appears to Clark on his birthday and instructs him that he needs to kill Lionel Luthor because Lionel knows his secret. Meanwhile, Lionel comes clean to Martha about his knowledge of Clark's secret since his possession by Jor-El, and some of his scribblings from his now-telepathic link to Jor-El are revealed to announce that the "Vessel of Zod" is coming. Meanwhile, Lex has another meeting with Milton Fine who tells Lex that he is trying to make a vaccine to protect mankind against an alien virus. When Lana expresses suspicion that Fine is not who he appears to be, Fine reveals his real identity and that "Jonathan Kent" is just another copy of Fine (The Brainiac) sowing seeds of anxiety in Clark.

After "being prepared" by Fine, Lex is abducted in a field by a strange light. Meanwhile, Clark goes to the Fortress of Solidude where the spirit of Jor-el gives a dagger to Clark and advises him to destroy Lex, who would be the vessel of the spirit of Zod outside the Phantom Zone in which Fine, the Brain-Interactive-Construct, is trying to release. Martha travels with Lois to Washington in an airplane of the Luthorcorp. When Zod is released, he possesses Lex, and traps Clark in the Phantom Zone. Fine unleashes a powerful computer virus, creating chaos on Earth. Lois and Martha faint in the airplane without oxygen as another copy of Fine/Brainiac hijacks the plane. Chloe and Lionel are attacked by a raged crowd, while Lex/Zod and Lana declare their love for one another as both plan to travel their path together on the dark side...

While Clark is still frozen in the fortress, Bizarro grows closer to Lana, who returns the feelings on just as deep a level, even sharing some badly-needed information with him while he still attempts to carry out his intentions of destroying Clark. Lex's brother, Julian, reveals himself to Lionel in an effort to clear the air between all parties involved.

When Brainiac ends up in a confrontation with Clark after trying to coerce Kara into joining him, he takes it out on Lana.

Clark is shown by Jor-El what life on Earth would have been like, had he not sent him there instead of facing the doom of his fellow Kryptonians.

Clark feels that Kara is under the effects of red kryptonite when he discovers that she is the reason for the plane containing the last member of the Veritas exploding. Lex is directed to look for answers surrounding the traveler in the Arctic Circle, where Clark's Fortress of Solitude rests.

It's been four weeks since the Fortress collapsed and Clark disappeared. Green Arrow calls upon Black Canary and Aquaman to locate the missing Clark Kent. Clark, in the meantime, is powerless and residing in a Russian prison camp in Siberia. With Lex Luthor missing and presumed dead, a new ruthless CEO, named Tess Mercer, is appointed the head of LuthorCorp and moves into Lex's mansion with her own dark plans for Clark and Metropolis. Chloe is kidnapped by a clandestine group that has discovered her special powers and they want to test the limits of those new powers by locating Green Arrow and his friends.

When Chloe begins having memory loss when the essence of Brainiac begins replacing her memories with Kryptonian codes, Clark decides to use the Crystal of Knowledge to reconstruct the Fortress of Solitude and ask the spirit of Jor-El for help. Meanwhile, Jimmy begins to worry about Chloe's well-being, while Davis, disturbed by the knowledge that he may have alien origins, begins to become drawn to Chloe.

Still gravely pondering his place in life, Clark lets Lois drag him along to their Smallvillle high school reunion. Rather than enjoying his hero status, while Lois shines less than she expected, Clark worries when he spots Brainiac, but it turns out he returned from the future with the Legions ring to show Clark how vital his contribution is to prevent a horrible future for him, Oliver, their friends and the world.

The story of Clark Kent culminates in this two-hour series finale as Clark takes the last step to becoming the Man of Steel.